Analysis of avian pathogenic Escherichia Coli (APEC) and its antimicrobial resistance risk characteristics and critical control points in laying hens

For precise prevention and control of Avian Pathogenic Escherichia coli (APEC) and its antimicrobial resistance (AMR) transmission in egg-laying hen farming, this study analyzed the prevalence, resistance characteristics, and risk sources of APEC in 614 samples from layer farms using antimicrobial susceptibility testing and whole-genome sequencing(WGS). Key findings include:APEC prevalence exhibited significant spatiotemporal heterogeneity, with the isolation rate peaking during the egg-laying period in August. APEC was primarily enriched in high-organic matter environments like the cloaca, manure waste, and flies. Among resistance genes, tet(A) (tetracyclines) had the highest detection rate, followed by floR (florfenicol) and sul2 (sulfonamides); mcr-1.1 (colistin) was also detected. Resistance genes for six classes of antibiotics, including ampicillin, showed a significant positive correlation with their corresponding phenotypic resistance (P < 0.05). All strains carried mobile genetic elements, with the plasmid IncFIB(AP001918) present in 87.2 % of isolates. Elements such as the IS575-aph-sul2 complex, Tn2- bla_TEM, and ISVsa3 drove multidrug resistance transmission, with water sources and eggshells serving as important resistance gene reservoirs. A total of 22 sequence types (STs) were identified, with ST69, ST162, and ST155 being the predominant types. Core genome MLST (cgMLST) and single nucleotide polymorphism (SNP) traceability analysis confirmed: ST69 (cgST115177) was highly homologous (≤ 2 allelic differences) between feed and fecal samples, indicating feed as a risk source; ST162 (cgST130769) was homologous (≤ 4 allelic differences) among eggshells, air, and wall samples, suggesting horizontal transmission within the farm; and strains of cgST87293 in water sources indicated cross-farm transmission. This study reveals the AMR risk characteristics of APEC in layer farms and identifies key control points, highlighting the urgent need to strengthen precise prevention and control guided by the "One Health" concept.